Packaging fixes.

.gitlab-ci.yml

@@ -11,9 +11,10 @@ before_script:
     - apt-add-repository universe
     - apt-get update
     - apt-get install -y python3 python3-pip make python3-numpy python3-matplotlib hmmer 
-    - alias python=python3; pip3 install --upgrade pip sphinx sphinx-argparse sphinx_rtd_theme pytest pandas
-    - hash -r pip3
-    - alias python=python3; pip3 install -e ./
+    - alias python=python3; pip install --upgrade pip
+    - alias python=python3; pip install sphinx sphinx-argparse sphinx_rtd_theme pytest pandas
+    - hash -r pip
+    - alias python=python3; pip install -e ./
 
 
 do_testing:

MANIFEST.in

@@ -1,8 +1,10 @@
 
 include README.md
-include LICENSE
+include LICENSE.md
 
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
+rerursive-include pychopper/phmm_data *.*
+rerursive-include pychopper/primer_data *.fas
 recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

scripts/cdna_classifier.py

@@ -12,8 +12,9 @@
 
 from pychopper import seq_utils as seu
 from pychopper import utils
-from pychopper import phmm_data, primer_data
 from pychopper import chopper, report
+import pychopper.phmm_data as phmm_data
+import pychopper.primer_data as primer_data
 
 
 """

setup.py

@@ -33,9 +33,12 @@
     url='',
     packages=[
         'pychopper',
+        'pychopper.phmm_data',
+        'pychopper.primer_data'
     ],
     package_dir={'pychopper':
                  'pychopper'},
+    package_data={'pychopper': ['primer_data/*.fas', 'phmm_data/*.*']},
     include_package_data=True,
     install_requires=requirements,
     zip_safe=False,